Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

Paloma Cejas, Yotam Drier, Koen M.A. Dreijerink, Lodewijk A.A. Brosens, Vikram Deshpande, Charles B. Epstein, Elfi B. Conemans, Folkert H.M. Morsink, Mindy K. Graham, Gerlof D. Valk, Menno R. Vriens, Carlos Fernandez del Castillo, Cristina R. Ferrone, Tomer Adar, Michaela Bowden, Holly J. Whitton, Annacarolina Da Silva, Alba Font-Tello, Henry W. Long, Elizabeth GaskellNoam Shoresh, Christopher M. Heaphy, Ewa Sicinska, Matthew H. Kulke, Daniel C. Chung, Bradley E. Bernstein, Ramesh A. Shivdasani*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

117 Scopus citations


Most pancreatic neuroendocrine tumors (PNETs) do not produce excess hormones and are therefore considered ‘non-functional’1–3. As clinical behaviors vary widely and distant metastases are eventually lethal2,4, biological classifications might guide treatment. Using enhancer maps to infer gene regulatory programs, we find that non-functional PNETs fall into two major subtypes, with epigenomes and transcriptomes that partially resemble islet α- and β-cells. Transcription factors ARX and PDX1 specify these normal cells, respectively5,6, and 84% of 142 non-functional PNETs expressed one or the other factor, occasionally both. Among 103 cases, distant relapses occurred almost exclusively in patients with ARX+PDX1 tumors and, within this subtype, in cases with alternative lengthening of telomeres. These markedly different outcomes belied similar clinical presentations and histology and, in one cohort, occurred irrespective of MEN1 mutation. This robust molecular stratification provides insight into cell lineage correlates of non-functional PNETs, accurately predicts disease course and can inform postoperative clinical decisions.

Original languageEnglish (US)
Pages (from-to)1264-1269
Number of pages6
JournalNature Medicine
Issue number8
StatePublished - Aug 1 2019

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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